Life Science 3

Introduction of Molecular Biology

Instructor: April Pyle, Ph.D. (1st half) and Randy Wall, Ph.D. (2nd half)
Textbook: Watson 7th edition- Molecular Biology of the Gene

Administration issues please see: Life Sciences Core Curriculum Office

Hershey Hall Room 222
Office Hours: Monday-Friday 9-12PM & 1-4PM
Email: lscore@lifesci.ucla.edu

Syllabus

Course Material
Lecture notes- powerpoint slides/course notes
Text book (Watson 7th edition)- only for additional
reading
Audio/Video podcasts
https://ccle.ucla.edu/ (Course website)

Grading- 2 EXAMS
Pyle

May 4

Midterm Exam (5-7:50pm)

Wall

June 11

Final Exam (8-11am)

Make-up Policy:
No make up examination will be given. If you are unable to take an
examination due to illness or other emergency, you are responsible for
contacting the Life Sciences Core Curriculum Office before the
examination. You are required to have written verification from a physician
regarding the illness or emergency.

Policies
Exams will cover predominately lectures and textbook
as a reference.
Re-grade requests are accepted only with demonstrated
error (rare). Requests must be submitted to Core office
by Friday of week following exam with typed
explanation of issue.
Entire exam will be re-graded by TA.
Exams will be left with the TA.
No excuses for missing exam. No-Make-up examscontact LS Core if emergency.

Office Hours and Class Help

Pyle Office Hours: Thurs (3:30-5)

BSRB (Basic Science Replacement Bldg)

Life Sciences Core Curriculum Office

277A (office)

Hershey Hall Room 222

Office Hours: Monday-Friday 9-12PM

& 1-4PM

Email: lscore@lifesci.ucla.edu

LS3 TAs: (see TAs for office hrs)

Yuqian Chen
angelachen0225@g.ucla.edu
Yasmin Ghochani yghochani@ucla.edu
Soyon Kim
soyonkim@ucla.edu
Julia Lipianskaya jlipianskaya@ucla.edu
Brittany Ulrich
bulrich@ucla.edu

LS3 TUTORS

Peer Learning

https://www.lscore.ucla.edu/lsplf.php

Assessment (not graded): Surveys via email and Concept Inventory (CI) exam will be
given in discussion sections (1st and 10th week) to assess class learning in LS3. This
is not a part of your grade but participation would be appreciated.

Lecture
1

Molecular Components

March 31, 2015

Pyle

Why study molecular biology?

Molecular biology seeks to

understand the physical
and chemical basis of life.
Growth
Division
Specialization
Movement
Interactions

Cell: the Basic Unit Of Living Organisms

Mouse

Xenopus

C. Elegans

Bacteria

Drosophila

Yeast

Plants

Example Prokaryotic Cell

Features in Bacteria

Eukaryotic Key Features of Complexity

-Complex Nuclear Structure
-Chromosome compaction/
accessory proteins
-Complex membrane organelles
-Complex cytoskeletal components
-Increased Plasma membrane
complexity and activity of protein
Regulation (secretory, vesicles,
Transport)
-Nobel Prize in Medicine awarded to
Rothman, Schekman, and Sdof-2013
for this work!! (vesicles and
transport in cells)
-Integrated and controlled cell
cycle
-Increase in enzymes regulating
key aspects of molecular biology

Eukaryotic Cell Structure and Function

Cytoskeleton- Motility:composed of microtubules,
Microfilaments and intermediate filaments.
Ribosome-large complex of RNA molecules, the
Engine of protein synthesis or translation
Lysosome-small organelle, functions in degradation
of materials internalized by endocytosis/autophagy
Golgi complex-stacks of flattened, interconnected
Compartments that function in processing and sorting
of proteins and lipids
Nucleus- houses DNA organized into chromosomes,
synthesis of RNA and ribosome assembly
Smooth endoplasmic reticulum-lacks ribosomes,
functions in lipid synthesis
Rough endoplasmic reticulum-associated with
ribosomes, functions in synthesis and processing of
secreted and membrane proteins
Mitochondria- powerhouse organelle that produces
most ATP (energy) of cell
Nucleolus-site of rRNA synthesis, processing and
ribosome subunit assembly
Chromatin-complex of DNA, histones, and non histone
Proteins from which chromosomes are formed
Plasma membrane- lipid and protein bilayer of cell
membrane

The operating system of life..

Cells are almost like
tiny factories run by
robots, with the
nucleus, DNA,
proteins, lipids,
vitamins and
minerals all playing
critical roles.
In this TED ED,
George Zaidan and
Charles Morton lay
out the blueprint of a
cell and explain how
molecular binds all
life together.

http://ed.ted.com/lessons/the-operating-system-of-life-george-zaidan-and-charles-morton

Macromolecules are the

building blocks of every cell

All cells are made up of the

same kinds of macromolecules
DNA - Deoxyribonucleic acid, stores information as genes
RNA - Ribonucleic acid, used for information transfer from DNA
to protein
Protein -functional molecules involved in all cellular processes
Lipids- diverse group of naturally occurring organic compounds
that are related by their solubility in nonpolar organic solvents
and insolubility in water, ex. fatty acid, phospholipids
Polysacharrides-a carbohydrate composed of many
monosaccharide units, ex. starch, glycogen, and cellulose

Biomolecules in cells are the chemical

basis of all organisms

Microscopy:
Visualizing Cells and
Cell Components
Electron Microscopeviruses, lipids, actin,
DNA
Light Microscopebacteria, cells,
mitochondria
Human Vision- eggs,
embryos, mice

Macromolecules
Macromolecules have a
mass of greater than a few
thousand daltons
Typically have a higher
order structure
Chemical interactions
regulate stability of
macromolecules

Atoms in Macromolecules
Six most popular
atoms in living
systems:
Hydrogen,
Carbon,
Nitrogen,
Phosphorus,
Oxygen
Sulfur

Types & Properties of Chemical bonds

that regulate the interaction between
two atoms:
!!

Covalent bonds

------

Two atoms interact by sharing electrons!

Strong, hold atoms in a molecule together (intra-molecular bonding)!
Bond strength is ~110 kcal / mol, it is the energy needed to break a bond, !
Single bond: two atoms sharing 1 pairs of electrons, free rotate!
Double bonds: two atoms sharing 2 pairs of electrons, can not rotate!

-- Interactions

!Noncovalent

bonds

!!

between atoms not involved with electron sharing!

-- weak bonds, but many working together can stabilize 3D structure of a!

large molecule (intra-molecular bonding). !
-- help molecules bind to other molecules (inter-molecule interactions).!
-- particularly important for biomolecules!

Examples of Covalent Bonds

Single bond

Double bond

Covalent bond vs ionic (noncovalent)

bond

Four types of noncovalent bonds

(1) Ionic bonds

- attractive force between

positively and negatively
charged atoms
- in ionic bonds, atoms gain
or lose electrons completely
to its partner
-strongest noncovalent bond

(2) Hydrogen bonds

-H bond is the electrical attraction between a
hydrogen atom of one molecule and negatively
charged atom in another molecule. It forms
when a hydrogen atom is sandwiched
between two electron-attracting atoms such
as O and N.
e.g. O-H.O, N-HO,
- H bond is particularly important for the
high-order structures of polymers such as
the secondary structure of protein and RNA
and the double strand structure of DNA.
- H2O molecules (in water) stick to each
other and others by H bonds.

(3) Hydrophobic interactions

-force that causes nonpolar portions of molecules to stay away from
water molecules
-In contrast to other bonds that form because the two parties love
each other, the hydrophobic interaction is formed because
all parties hate water and they all get pushed together.
the enemy of my enemy is my friend

(4) Van der Waal Forces

-Weak attractive forces
through transient dipoles
in the electron clouds of
all atoms.
-Attraction decreases
rapidly with increasing
distance.
However, atoms repel
one another when they
are too close.

Examples of Non-Covalent Bonds

Distribution of Living Matter Components

Examples of Small molecules or

biomolecules that make up the
subunits of macromolecules
- Sugar:

glucose, ribose, etc

- fatty acid:

oleic acid (C18), etc

- Amino acids:

glycine, methione, etc

- base:

adenine (A), guanine (G),

cytosine (C), thymine (T), uracil (U)

Macromolecules are polymers made up of

individual subunits or monomers

Functional Groups give

Biomolecules Unique Properties

Functional groups can change:

Physical properties
Chemical reactivity
Solubility in solution
Two common functional bonds are:
Ester bonds
Amide bonds

Schematic of Polymer
Formation

-In hydrolysis, water is added to break covalent bond between monomers and in
condensation, water is removed to bond them together.
-Condensation reactions store energy and hydrolysis typically releases energy

Both covalent and non-covalent bonds are involved

in formation of a macromolecular complex

Four most important macromolecules of cells

Polymer--Many copies of small biomolecules (monomer) linked
covalently to form polymers, MWs are often in kD (103 Dalton).
Polysaccharide polymers of sugars
Polysaccharides are structure and energy materials of the cell.!
Proteins polymers of amino acids, often measured by kilodalton
(kD). Proteins are the workforce of the cell.
DNA/RNApolymers of deoxyribonucleotides/ribonucleotides
DNA/RNA are the genetic material of the cell.

lipidmajor classes: fatty acids, phospholipids, steroids, and
triglycerides- important for enery storage and make up the cell
membranes.

Where are biomolecules

found in the cell?

How do we get from one

cell to Einstein?
?

1 Cell!

14!

10!

Cells!

Cell Division and Differentiation!!

Cell in Metaphase during Division

Differentiated Neurons

Cell Division
A process by which a cell
duplicates its own material and
divides into two cells."
"G1"
"G2/M"
"S"
What happens if the cell
progresses abnormally through
this cycle??"

Movie of human embryonic development

Differentiation: A process by which a cell

undergoes a change to become a specialized cell
type
What are the gene regulatory mechanisms that specify this change?

~ 20,000 genes!
~ 20,000 genes!

SubTypes of Cell Differentiation:

Specialized Cells have Unique Cell Functions

What happens if your cells become diseased?

Differentiated Cells Can be used for Cell Replacement
Therapy

Somatic Cell Nuclear Transfer or Human

Embryonic Stem Cell Based Therapies

Induced Pluripotent Stem Cells (iPSCs &

Cell Replacement Therapy

Central Dogma of Molecular

Biology

Transcription

DNA

Translation

RNA

Protein

Macromolecules are key players that regulate every aspect of molecular biology!

Course Overview
1. Structure and function of
DNA, RNA, and protein
2. Basic Molecular Biology Processes
Replication
Transcription
Translation
Regulation of gene expression
Genetic variations
Transcriptome and RNA silencing
3.

Molecular Biology Methods

Protein purification and analysis
Recombinant DNA technology

Implications & Critical Thinking-1

DNA is the building block of genes
Genes are linked to chromosomes
Diversity can be generated by mutations in the DNA sequence
Mutations can also lead to disease
What happens if mutations occur in the DNA sequence?
How does a mutation at the gene level affect the protein?